|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Mar 31, 2014 |
Title |
Chimpanzee_3 |
Sample type |
SRA |
|
|
Source name |
Prefrontal Cortex
|
Organism |
Pan troglodytes |
Characteristics |
tissue: Prefrontal Cortex organism: chimpanzee
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was isolated using Trizol reagent (Cat. No. 15596-026, Invitrogen). The libraries were constructed from the isolated total RNA according to the "TruSeq RNA Sample Preparation Kit" protocol (www.illumina.com) without modification. As the protocol includes the procedure of enrichment for the mRNA, an additional polyA selection was not necessary. RNA libraries were prepared for sequencing using Illumina TruSeq protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Illumina Casava1.7 software used for basecalling, and only the ones passing illumina quality controls were retained. Reads were mapped onto correponding reference genomes (hg19, panTro3) by Tophat-1.4.1, with parameters: -a 8 -m 2 no-coverage-search microexon-search segment-mismatches 3 segment-length 25. We made a reciprocal lift-over between chimpanzee and human (Ensembl annotation v. 69, coding exons only), and used only exons that could be lift-overed to calculate RPKMs for each gene. Then quantile normalization was applied, and each gene was z-transformed. Genome_build: hg19, panTro3 Supplementary_files_format_and_content: tab-delimited text files including expression measurements for each gene from each sample.
|
|
|
Submission date |
Mar 18, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Liu He |
E-mail(s) |
heliu@picb.ac.cn
|
Organization name |
PICB
|
Street address |
320 Yue Yang Road
|
City |
Shanghai |
ZIP/Postal code |
200031 |
Country |
China |
|
|
Platform ID |
GPL16809 |
Series (1) |
GSE45263 |
Increased Neanderthal ancestry in genomic regions associated with lipid catabolism in contemporary Europeans |
|
Relations |
SRA |
SRX252099 |
BioSample |
SAMN01983972 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
|